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iqbal-lab-org
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minos
Variant call adjudication
MIT License
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hardcoded ram limit for one step of multisample workflow
#74
iqbal-lab
closed
4 years ago
0
Parallelised build in nextflow
#73
bricoletc
closed
5 years ago
9
multi-sample pipeline: parallelise (nextflow) chunk building
#72
iqbal-lab
closed
5 years ago
3
Do not use unmapped reads in split pipeline
#71
martinghunt
closed
5 years ago
0
Implement filtering
#70
martinghunt
closed
5 years ago
0
multi sample pipeline: ALT allele list in final VCF differ between samples/files
#69
kerrimalone
closed
4 years ago
7
Filter on depth and gt conf percentile
#68
martinghunt
closed
5 years ago
4
Option to not use unmapped reads in multi sample pipeline
#67
martinghunt
closed
5 years ago
2
Check if whitespace in seq names breaks minos
#66
martinghunt
closed
2 years ago
2
Call filtering
#65
martinghunt
closed
5 years ago
0
Add Ns to flanks when evaluating recall to avoid issues where truth p…
#64
rmcolq
closed
5 years ago
0
Update dnadiff_mapping_based_verifier and evaluate_recall in line with other recent minos changes
#63
rmcolq
closed
5 years ago
0
Fix off by one error reading BED files
#62
martinghunt
closed
5 years ago
0
Check with ref improvements
#61
martinghunt
closed
5 years ago
0
Fix tests for cluster_vcf_records 0.9.1
#60
martinghunt
closed
5 years ago
0
Call filtering
#59
martinghunt
closed
5 years ago
0
add `max_soft_clipped parameter` to recall functions
#58
rmcolq
closed
5 years ago
0
Tidy test files and prints
#57
martinghunt
closed
5 years ago
0
Fix mask
#56
rmcolq
closed
5 years ago
0
Add allow ref alleles option
#55
rmcolq
closed
5 years ago
0
use gramtools build --all-kmers. Default k=10. Use k=5 for tests
#54
martinghunt
closed
6 years ago
0
Save ram multi pipeline cluster
#53
martinghunt
closed
6 years ago
0
Bug fixes if only TPs or FPs found
#52
martinghunt
closed
6 years ago
0
Add dp and gt conf plots
#51
martinghunt
closed
6 years ago
0
quasimap use --output-directory instead of --run-directory
#50
martinghunt
closed
6 years ago
0
Check with ref use edit distance
#49
martinghunt
closed
6 years ago
0
gramtools quasimap `--run-directory` deprecated
#48
martinghunt
closed
6 years ago
0
Speedup bcftools merge
#47
martinghunt
closed
6 years ago
0
remove cortex MISMAPPED_UNPLACEABLE VCF records
#46
martinghunt
opened
6 years ago
1
Exclude regions to verify
#45
martinghunt
closed
6 years ago
0
if chunking VCF, check bam is indexed
#44
martinghunt
opened
6 years ago
0
Gramtools build tweaks
#43
martinghunt
closed
6 years ago
0
Multithread vcf chunker
#42
martinghunt
closed
6 years ago
0
Implement multithreading gramtools build vcf chunks
#41
martinghunt
closed
6 years ago
0
split by allele count
#40
martinghunt
closed
6 years ago
0
Multi sample keep zero cov
#39
martinghunt
closed
6 years ago
0
multi sample pipeline keep zero cov alleles
#38
martinghunt
closed
6 years ago
0
Gramtools error checking
#37
martinghunt
closed
6 years ago
0
Add max_alleles_per_cluster option
#36
martinghunt
closed
6 years ago
0
stop if not running anything
#35
martinghunt
closed
6 years ago
0
Logging improvements
#34
martinghunt
closed
6 years ago
0
Remove zero cov alleles
#33
martinghunt
closed
6 years ago
0
Chunk variants
#32
martinghunt
closed
6 years ago
0
Implement chunking the reference genome
#31
martinghunt
closed
6 years ago
2
multi_sample_pipeline limit max alleles
#30
martinghunt
closed
6 years ago
0
multi_sample_pipeline --norun FileNotFoundError
#29
martinghunt
closed
6 years ago
0
Add support for large variant calls in multi-sample pipeline
#28
martinghunt
opened
6 years ago
0
Logging issues
#27
martinghunt
closed
6 years ago
0
Multi sample filter vcf
#26
martinghunt
closed
6 years ago
0
Nextflow memory options
#25
martinghunt
closed
6 years ago
0
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